<html>
<title>Build counts file</title>
<body style="padding:20px;width:650px;font-family:Times">
<h3>Build counts file</h3>

Often the read counts for each library (or replicate) are provided in separate files,
which need to be combined into one table for import into TCW. This interface is designed
to make that easier. 
<p>
To use this interface, your count files need to have a two-column format without headers:
<pre>
Sequence_name1	count1
Sequence_name2	count2
...
</pre>

<p>
<table border=0 cellspacing=4 cellpadding=3>
<tr><td valign="top" nowrap>Add Folder of Libs<td>Go to the directory with your count files and
select "Open". All files will be checked for the correct format, and the correct ones will be 
entered into the table. Use "Edit Lib" to change the Lib name.
<tr><td valign="top" nowrap>Add lib<td>To add one count file, select the file and enter a "Lib name",
which is the name of its library or replicate, e.g. "Root5", for Root library, 5th
replicate. 
<tr><td valign="top" nowrap>Edit lib<td>You cannot directly edit the table, but select a row followed
 by Edit allows you to edit the Lib name or File name.
<tr><td valign="top" nowrap>Remove lib<td>Select a row to remove it.
<tr><td valign="top" nowrap>Save<td>If you are not ready to execute "Generate File", but want to 
save what you have done, select "Save". You can exit runSingleTCW and come back into this menu
and the information will be preserved. 
<tr><td valign="top" nowrap>Generate File<td>The file "Combined_read_counts.csv" will be generated,
which will have one column for each of your original files, with the specified Lib names as headers.
This will be entered as the Read Count File in the Library Add/Edit panel, and when you press "Keep"
on that panel, the information will be transferred to the main window.
</table>